Re: [galaxy-dev] python2.6?
Yamshchikov, Vladimir wrote: > Hello all, > > If this question is not for this list, please advise. Both my RHEL55 and SL55 > are based on python 2.4.3 - how I can add python 2.6 support for Galaxy > without screwing up OS? I had both 2.4 and 2.6 installed, by python -V > returns only 2.4.3. When I uninstalled 2.4.3, SL55 self-destructed, the same > will happen with RHEL55. I was advised that 2.6 should not ever be made seen > (like manipulating $PATH) by the system that depends on 2.4 - so how I add > 2.6 if it is needed for full functionality? Hi Vladimir, You could install 'python26' from EPEL[1], presumably this does not break /usr/bin/python since it installs the new version as /usr/bin/python2.6. Then as the user which runs Galaxy, do something like this: $ mkdir $HOME/bin $ ln -s /usr/bin/python2.6 $HOME/bin/python $ export PATH=$HOME/bin:$PATH $ echo 'export PATH=$HOME/bin:$PATH' >> $HOME/.bash_profile --nate [1] http://fedoraproject.org/wiki/EPEL > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] python2.6?
Hello all, If this question is not for this list, please advise. Both my RHEL55 and SL55 are based on python 2.4.3 - how I can add python 2.6 support for Galaxy without screwing up OS? I had both 2.4 and 2.6 installed, by python -V returns only 2.4.3. When I uninstalled 2.4.3, SL55 self-destructed, the same will happen with RHEL55. I was advised that 2.6 should not ever be made seen (like manipulating $PATH) by the system that depends on 2.4 - so how I add 2.6 if it is needed for full functionality? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] python2.6 UserWarning: Unbuilt egg for pytz
Vipin TS wrote:
> Hi all,
>
> Last day we upgraded our galaxy service computing cluster nodes operating
> system from Ubuntu hadry to lucid 10.4. We updated python eggs and now
> getting an Warning message, it apparently kills the galaxy jobs. Warning
> message as follows:
>
> /home/abc/galaxy/lib/galaxy/eggs/__init__.py:332: UserWarning: Unbuilt
> egg for pytz [unknown version] (/usr/lib/python2.6/dist-packages)
> env = pkg_resources.Environment( platform=pkg_resources.get_platform() )
>
> >From the warning message I can see that the problem with unbuilt egg for
> pytz module. Before approaching you I googled the same and got a good thread
> which explains similar kind of issues (
> https://bugs.launchpad.net/ubuntu/+source/distribute/+bug/576434). I
> followed #9 from TJ and made a work around and unfortunately no luck. Does
> anyone had a problem with this before, if yes I like to hear from you that
> how do u managed to get rid of the warning message.
Hi Vipin,
If you haven't come up with a solution for this from the Ubuntu side, there
should at least be a workaround within Galaxy (this is untested).
In lib/galaxy/eggs/__init__.py, somewhere near the top:
import warnings
inside get_env():
def get_env():
with warnings.catch_warnings():
warnings.simplefilter("ignore")
env = pkg_resources.Environment( search_path='',
platform=pkg_resources.get_platform() )
for dist in pkg_resources.find_distributions( os.path.join( galaxy_dir,
'eggs' ), False ):
env.add( dist )
return env
--nate
>
> Many thanks,
>
> Vipin T S
> Friedrich Miescher Laboratory
> of the Max Planck Society
> Spemannstrasse 39, 72076
> Tuebingen, Germany
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[galaxy-dev] python2.6 UserWarning: Unbuilt egg for pytz
Hi all, Last day we upgraded our galaxy service computing cluster nodes operating system from Ubuntu hadry to lucid 10.4. We updated python eggs and now getting an Warning message, it apparently kills the galaxy jobs. Warning message as follows: /home/abc/galaxy/lib/galaxy/eggs/__init__.py:332: UserWarning: Unbuilt egg for pytz [unknown version] (/usr/lib/python2.6/dist-packages) env = pkg_resources.Environment( platform=pkg_resources.get_platform() ) >From the warning message I can see that the problem with unbuilt egg for pytz module. Before approaching you I googled the same and got a good thread which explains similar kind of issues ( https://bugs.launchpad.net/ubuntu/+source/distribute/+bug/576434). I followed #9 from TJ and made a work around and unfortunately no luck. Does anyone had a problem with this before, if yes I like to hear from you that how do u managed to get rid of the warning message. Many thanks, Vipin T S Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
